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GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis

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Abstract

GDSL esterase/lipase proteins (GELPs), a very large subfamily of lipolytic enzymes, have been identified in microbes and many plants, but only a few have been characterized with respect to their roles in growth, development, and stress responses. In Brassica crops, as in many other species, genome-wide systematic analysis and functional studies of these genes are still lacking. As a first step to study their function in B. rapa ssp. pekinensis (Chinese cabbage), we comprehensively identified all GELP genes in the genome. We found a total of 121 Brassica rapa GDSL esterase/lipase protein genes (BrGELPs), forming three clades in the phylogenetic analysis (two major and one minor), with an asymmetrical chromosomal distribution. Most BrGELPs possess four strictly conserved residues (Ser-Gly-Asn-His) in four separate conserved regions, along with short conserved and clade-specific blocks, suggesting functional diversification of these proteins. Detailed expression profiling revealed that BrGELPs were expressed in various tissues, including floral organs, implying that BrGELPs play diverse roles in various tissues and during development. Ten percent of BrGELPs were specifically expressed in fertile buds, rather than male-sterile buds, implying their involvement in pollen development. Analyses of EXL6 (extracellular lipase 6) expression and its co-expressed genes in both B. rapa and Arabidopsis, as well as knockdown of this gene in Arabidopsis, revealed that this gene plays an important role in pollen development in both species. The data described in this study will facilitate future investigations of other BrGELP functions.

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Acknowledgments

This research was supported by research grants from Golden Seed Project (Center for Horticultural Seed Development, nos. 213003-04-3-CG100 and 213003-04-3-SB230), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), and Rural Development Administration (RDA).

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Authors and Affiliations

  1. Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Taejon, Republic of Korea

    Xiangshu Dong, Hankuil Yi & Yoonkang Hur

  2. Department of Life Science, Sogang University, Seoul, 100-611, Republic of Korea

    Ching-Tack Han

  3. Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea

    Ill-Sup Nou

  4. School of Agriculture, Yunnan University, Kunming, Yunnan, China

    Xiangshu Dong

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  1. Xiangshu Dong
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Correspondence to Yoonkang Hur.

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Conflict of interest

Dong X declares that he has no conflict of interest. Yi H declares that he has no conflict of interest. Han C-T declares that he has no conflict of interest. Nou I-S declares that he has no conflict of interest. Hur Y declares that he has no conflict of interest.

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Communicated by S. Hohmann.

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438_2015_1123_MOESM1_ESM.rar

Supplementary Table 1. Characteristics of the Chinese cabbage (Brassica rapa) GELP candidate genes, its pseudoenzymes and genes coding for muti-domain proteins. Supplementary Table 2. Characteristics of the Arabidopsis GELP candidate genes, its pseudoenzymes and genes coding for muti-domain proteins. Supplementary Table 3. Conserved motifs identified in the BrGELP proteins. Supplementary Table 4. Orthologous GELP genes in B. rapa and Arabidopsis. Supplementary Table 5. List of genes co-expressed with BrEXL6, with the Pearson’s correlation coefficient (PCC) threshold value set at 0.85.  ESTs co-expressed with all BrEXL6 probes, Brapa_ESTC003525, Brapa_ESTC000535 and Brapa_ESTC010981, were included. Supplementary Table 6. List of genes co-expressed with AtEXL6, with the Pearson’s correlation coefficient (PCC) threshold value set at 0.85. Supplementary Fig. 1 Gene structures of the BrGELPs and BrGELP pseudoenzymes. Exon/intron structures of 121 genes and 29 pseudoenzymes are presented. Green boxes represent exon regions, and solid lines indicate intron regions. Supplementary Fig. 2 Multiple sequence alignment of BrGELP and AtGELP genes. Supplementary Fig. 3 Phylogenetic relationships among the BrGELP and AtGELP gene families. Multiple protein sequence alignment was performed using ClustalW implemented in MEGA6. For this tree, the initial tree were generated by implementing NJ/BioNJ method, and tree improvement was achieved by Nearest-Neighbor-Interchange (NNI) and branch support analysis by 1000 replicates bootstrap. Different clades and branches (subclades) are indicated by the colors of the background and branch lines, respectively. Supplementary Fig. 4 Heat map representation and hierarchical clustering of BrGELP genes (A) and its pseudoenzymes (B) across root, stem, and leaf. Heat maps were generated from RPKM values (Cheng et al. 2012) using the MeV software. NA, no available data. Supplementary Fig. 5 A, Whole anthers of wild-type and AtEXL6-transgenic plants stained with modified Alexander solution (Peterson et al. 2010). Bar, 40 μm. B, Overall plant morphology of the AtEXL6-antisense and -sense transgenic lines. Bar, 50 mm. (RAR 64997 kb)

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Dong, X., Yi, H., Han, CT. et al. GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis. Mol Genet Genomics 291, 531–542 (2016). https://doi.org/10.1007/s00438-015-1123-6

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